A microscopic scenario on recovery mechanisms under waterlogging and submergence stress in rice

MAIN CONCLUSION

Adaptive traits in rice responding to flooding, a compound stress, are associated with morpho-anatomical and physiological changes which are regulated at the genetic level. Therefore, understanding submergence stress tolerance in rice will help development of adapted cultivars that can help mitigate agricultural losses. Rice is an important dietary component of daily human consumption and is cultivated as a staple crop worldwide. Flooding is a compound stress which imposes significant financial losses to farmers. Flood-affected rainfed rice ecosystems led to the development of various adaptive traits in different cultivars for their optimal growth and survival. Some cultivars can tolerate hypoxia by temporarily arresting elongation and conserving their energy sources, which they utilize to regrow after the stress conditions subside. However, few other cultivars rapidly elongate to escape hypoxia using carbohydrate resources. These contrasting characters are regulated at the genetic level through different quantitative trait loci that contain ERF transcription factors (TFs), Submergence and Snorkels. TFs can simultaneously activate the transcription of various genes involved in stress and development responses. These TFs are of prime importance because the introgressed and near-isogenic lines showed promising results with increased submergence tolerance without affecting yield or quality. However, the entire landscape of submergence tolerance is not entirely depicted, and further exploration in the field is necessary to understand the mechanism in rice completely. Therefore, this review will highlight the significant adaptive traits observed in flooded rice varieties and how they are regulated mechanistically.

Physician-Modified Endografts Versus Chimney/Snorkel for Ruptured and Symptomatic Juxtarenal and Paravisceral Aneurysms in the Vascular Quality Initiative

OBJECTIVES

Ruptured and symptomatic juxtarenal and paravisceral aneurysms present technical challenges during endovascular repair. We sought to compare physician modification and fenestrated (PMEG) versus chimney/periscope/snorkel (CHIMPS) repair techniques for the treatment of ruptured and symptomatic paravisceral and juxtarenal aortic aneurysms (r/sPJAA).

METHODS

Patients in the thoracic and complex endovascular aneurysm module of the Vascular Quality Initiative (VQI) national registry undergoing CHIMPS and PMEG for r/sPJAA were included. Patients who underwent thoracic aneurysm repair with only celiac intervention or who had coverage or occlusion only of one renal or visceral branch vessel were excluded. One-year mortality was the primary outcome. Secondary outcomes included peri- and postoperative endoleak, hospital and ICU length of stay, reintervention, and other local and systemic complications.

RESULTS

A total of 81 CHIMPS and 47 PMEG patients were identified. Patients undergoing PMEG were more frequently symptomatic, had a history of CHF and were taking aspirin, statin and P2Y12 antiplatelet medications. Patients undergoing CHIMPS presented more frequently with rupture. There was no significant survival advantage for CHIMPS over PMEG patients (P = 0.5). There were no apparent long-term differences in the numbers of endoleaks or in the rates of subsequent reinterventions between the two groups.

CONCLUSIONS

It does not appear that the procedure type (CHIMPS versus PMEG) is associated with postoperative survival in patients with r/sPJAA. Not surprisingly, survival is associated with postoperative complications, particularly myocardial infarction and intestinal ischemia. Further research should evaluate reasons for failure to rescue from and the impact of postoperative complications on the postoperative survival after endovascular repair of r/sPJAA.

Extracting chemical reactions from text using Snorkel

Background

Enzymatic and chemical reactions are key for understanding biological processes in cells. Curated databases of chemical reactions exist but these databases struggle to keep up with the exponential growth of the biomedical literature. Conventional text mining pipelines provide tools to automatically extract entities and relationships from the scientific literature, and partially replace expert curation, but such machine learning frameworks often require a large amount of labeled training data and thus lack scalability for both larger document corpora and new relationship types.

Results

We developed an application of Snorkel, a weakly supervised learning framework, for extracting chemical reaction relationships from biomedical literature abstracts. For this work, we defined a chemical reaction relationship as the transformation of chemical A to chemical B. We built and evaluated our system on small annotated sets of chemical reaction relationships from two corpora: curated bacteria-related abstracts from the MetaCyc database (MetaCyc_Corpus) and a more general set of abstracts annotated with MeSH (Medical Subject Headings) term Bacteria (Bacteria_Corpus; a superset of MetaCyc_Corpus). For the MetaCyc_Corpus, we obtained 84% precision and 41% recall (55% F1 score). Extending to the more general Bacteria_Corpus decreased precision to 62% with only a four-point drop in recall to 37% (46% F1 score). Overall, the Bacteria_Corpus contained two orders of magnitude more candidate chemical reaction relationships (nine million candidates vs 68,0000 candidates) and had a larger class imbalance (2.5% positives vs 5% positives) as compared to the MetaCyc_Corpus. In total, we extracted 6871 chemical reaction relationships from nine million candidates in the Bacteria_Corpus.

Conclusions

With this work, we built a database of chemical reaction relationships from almost 900,000 scientific abstracts without a large training set of labeled annotations. Further, we showed the generalizability of our initial application built on MetaCyc documents enriched with chemical reactions to a general set of articles related to bacteria.

Parallel artificial and biological electric circuits power petroleum decontamination: The case of snorkel and cable bacteria

Degradation of petroleum hydrocarbons (HC) in sediments is often limited by the availability of electron acceptors. By allowing long-distance electron transport (LDET) between anoxic sediments and oxic overlying water, bioelectrochemical snorkels may stimulate the regeneration of sulphate in the anoxic sediment thereby accelerating petroleum HC degradation. Cable bacteria can also mediate LDET between anoxic and oxic sediment layers and thus theoretically stimulate petroleum HC degradation. Here, we quantitatively assessed the impact of cable bacteria and snorkels on the degradation of alkanes in marine sediment from Aarhus Bay (Denmark). After seven weeks, cable bacteria and snorkels accelerated alkanes degradation by +24 and +25%, respectively, compared to control sediment with no cable bacteria nor snorkel. The combination of snorkels and cable bacteria further enhanced alkanes degradation (+46%). Higher degradation rates were sustained by LDET-induced sulphide removal rather than, as initially hypothesized, sulphate regeneration. Cable bacteria are thus overlooked players in the self-healing capacity of crude-oil contaminated sediments, and may inspire novel remediation treatments upon hydrocarbon spillage.

Fenestrated Endovascular Aneurysm Repair versus Snorkel Endovascular Aneurysm Repair: Competing yet Complementary Strategies

Juxtarenal/pararenal aortic aneurysms and type IV thoracoabdominal aneurysms pose particular technical challenges for endovascular repair as they involve the visceral segment in addition to insufficient infrarenal neck for the use of standard endovascular aneurysm repair (EVAR) devices. To overcome these challenges, complex EVAR techniques have been developed to extend the proximal landing zone cephalad with maintaining perfusion to vital aortic branches, thereby broadening the applicability of endografting from the infrarenal to the suprarenal aorta. Complex EVAR can be divided into two broad categories: fenestrated endovascular aneurysm repair (FEVAR) and snorkel EVAR. FEVAR is a valid procedure with the standardized procedure, although it remains as a relatively complex procedure with a learning curve. Given time constraints for the custom fenestrated graft, snorkel EVAR may be an alternative for complex repairs in symptomatic or ruptured patients for whom custom-made endografts may not be immediately available. This article discusses these two most commonly used complex EVAR strategies.

The state of complex endovascular abdominal aortic aneurysm repairs in the Vascular Quality Initiative

BACKGROUND

Endovascular repair of complex abdominal aortic aneurysms has become increasingly common, but reports have mostly been limited to single centers and single devices.

METHODS

We studied all endovascular repairs of complex abdominal aortic aneurysms (zone 6 or caudal) from 2014 to 2018 in the Vascular Quality Initiative. This included all commercially available fenestrated endovascular aneurysm repair (FEVAR), chimney/snorkel repairs, and physician-modified endografts (PMEGs), exclusive of investigational device exemptions and clinical trial devices. We used inverse probability-weighted multilevel logistic regression to compare rates of perioperative outcomes including death, acute kidney injury (AKI), and major adverse cardiac events (MACEs; the composite of death/stroke/myocardial infarction) and Cox regression for long-term mortality.

RESULTS

During the study period, surgeons performed 1396 complex endovascular repairs: 1308 (94%) elective, 63 (4.5%) for symptomatic aneurysms, and 25 (1.8%) for rupture. The number of centers performing complex endovascular repairs expanded steadily from 39 in 2014 to 81 in 2017. There were 880 FEVAR (63%), 256 PMEG (18%), and 260 chimney/snorkel repairs (19%). In elective cases, 3214 visceral vessels were incorporated and revascularized; 120 repairs (9%) involved one vessel, 481 (38%) repairs involved two vessels, 560 (44%) involved three vessels, and 113 (9%) involved four vessels. The mean number of arteries incorporated was 2.5 ± 0.8, with PMEGs involving the most arteries (3.3 ± 0.8 for PMEG vs 2.5 ± 0.6 for FEVAR and 1.9 ± 0.9 for chimney/snorkel; P < .001). PMEGs were used to treat more extensive aneurysms, and more incorporated the celiac and superior mesenteric arteries. There was no change in aneurysm extent, but the length of proximal seal extended over time. Chimney/snorkel cases employed more arm or neck access, had longer procedure times, and used more contrast material. Rates of perioperative death (3.4% for FEVAR vs 2.7% for PMEG vs 6.1% for chimney/snorkel; P = .13) and AKI (17% vs 18% vs 19%; P = .42) were similar, but chimney/snorkel was associated with higher rates of stroke (0.8% vs 0.9% vs 3.3%; P = .03) and MACEs (6.1% vs 5.4% vs 11.7%; P = .02). After adjustment, rates of perioperative death, AKI, and overall complications remained similar, but chimney/snorkel was associated with significantly higher odds of stroke (odds ratio [OR], 7.3 [1.5-36.4]; P = .015), myocardial infarction (OR, 18.7 [2.6-136.8]; P = .004), and MACEs (OR, 11.1 [2.1-58.9]; P = .005). Overall survival after elective repair was 91% at 1 year and 88% at 3 years, with no difference between repair types in crude or adjusted analysis.

CONCLUSIONS

The Vascular Quality Initiative provides a unique opportunity to study the real-world application and outcomes of complex endovascular aneurysm repair. Perioperative morbidity appears to be higher after chimney/snorkel repair, but further study is needed to confirm these findings and to establish the durability of these novel technologies.

Adjunctive visceral artery chimney in patients undergoing Zenith Fenestrated aortic repair

OBJECTIVE

Visceral artery chimneys have been employed as an adjunct to endovascular aneurysm repair (EVAR) to treat short-neck infrarenal and juxtarenal aortic aneurysms for more than two decades. With the widespread introduction of fenestrated endovascular aneurysm repair by the Food and Drug Administration-approved Zenith Fenestrated endograft (ZFEN; Cook Medical, Bloomington, Ind) to the United States in 2012, clinicians gained the ability to apply the chimney technique to these custom devices for difficult anatomy. The purpose of this report was to demonstrate feasibility and to provide evidence on the performance of chimneys for the treatment of complex juxtarenal aneurysms that could not be adequately treated with ZFEN alone.

METHODS

A retrospective analysis was performed of a prospectively maintained institutional ZFEN database capturing 110 fenestrated endovascular aneurysm repairs from October 2012 to January 2018 to identify patients undergoing a concomitant visceral artery chimney. All patients with <12 months of follow-up were excluded from further analysis. Demographic, anatomic, intraoperative, perioperative, and follow-up characteristics were tabulated and analyzed.

RESULTS

Six patients met criteria and were included in this investigation. They were universally male with a mean age of 76.2 years at the time of ZFEN/chimney. Chimneys were placed in a total of six visceral arteries (n = 1 per patient) consisting of three renal arteries, two celiac arteries, and one accessory renal artery. Mean estimated blood loss and operative time were 283 mL and 298 minutes, respectively. Technical success was achieved in all cases. Two small type IA "gutter" endoleaks were detected early; both spontaneously resolved on follow-up. We observed no instances of chimney migration, stenosis, or thrombosis perioperatively or on follow-up. Two reinterventions were performed in these six patients; these consisted of a repeated renal stent for ostial stenosis at a main body fenestration and a common femoral artery endarterectomy and patch angioplasty for an access-related common femoral artery occlusion.

CONCLUSIONS

Use of ZFEN in conjunction with a singular chimney is safe, feasible, and durable in patients with difficult anatomy who do not meet instructions for use as demonstrated in this limited series.

Endovascular repair of complex Juxtarenal aortic aneurysm using a combined fenestrated endograft and chimney technique

Chimney EVAR (CHEVAR) and Fenestrated EVAR (FEVAR) are two options for management of very complex abdominal aortic aneurysm (AAA). While some anatomical factors may favor one strategy over the other, there are some cases where the anatomical challenges may require using a hybrid approach. We are reporting the case of an 84-year-old male with a 6.8×5.7cm infrarenal abdominal aortic aneurysm that arises immediately below the level of the renal arteries and extends down to just above the iliac bifurcation with occluded celiac and inferior mesenteric arteries and severe bilateral renal artery stenosis with caudally oriented right renal and cranially oriented left renal artery. This case shows that a combined strategy with fenestrated graft and Chimney stenting is feasible for aortic aneurysm repair and may offer a reasonable option for patients with very complex aortic anatomy.

A Novel Chimney Approach for Management of Horseshoe Kidney During EVAR

INTRODUCTION

Abdominal aortic aneurysms (AAAs) with coexisting horseshoe kidney (HSK) can be difficult to repair, with variable blood supply from the aorta and iliac/mesenteric vessels. Endovascular aneurysm repair (EVAR) has become a popular, less invasive approach to aneurysm care, and a chimney approach to EVAR (ChEVAR) has expanded its use to more complex anatomy. It is mandatory to maintain adequate perfusion to the HSK and visceral branches as part of the treatment of an AAA.

REPORT

A 61-year-old male with an HSK was incidentally found to have an infrarenal AAA that measured 6 cm on a non-contrast computed tomography (CT) scan performed originally for a urologic complaint. A diagnostic angiogram was performed to define arterial anatomy and he was found to have a large inferior mesenteric artery (IMA) arising 1 cm above the level of the aneurysm. ChEVAR was performed to preserve the IMA and flow to the HSK with a completion angiogram revealing patent renal arteries, IMA, and no evidence of an endoleak. Follow-up CT imaging demonstrated a Type II endoleak that resolved upon partial nephrectomy for a right-sided transitional cell carcinoma with resection of the arterial blood supply feeding the Type II endoleak.

DISCUSSION

IMA preservation via ChEVAR is technically feasible and was crucial to preserve blood supply via the IMA to the HSK. Partial nephrectomy treated the transitional cell carcinoma and resolved the Type II endoleak requiring no additional endovascular intervention. A unique treatment course demonstrated the benefits of less invasive interventions when repairing AAA with an HSK.